Hi Pei,
Thank you for the hint. When I try running mvn from ctakes root, the results
(install.out.txt) make more sense but there are still some things to fix.
Michal
-----Message d'origine-----
De : Chen, Pei [mailto:[email protected]]
Envoyé : May-14-15 9:38 PM
À : <[email protected]>
Objet : Re: [VOTE] Release Apache cTAKES 3.2.2 (rc2)
Hi Michal,
Thanks for testing... Just curious Have you tried running mvn from ctakes root
rather than the Ytex project sub directory?
C:\cTakes-3.2.2\ctakes\mvn install
Vs
C:\cTakes-3.2.2\ctakes\ctakes-ytex>mvn install
Sent from my iPhone
On May 14, 2015, at 8:37 PM,
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>> wrote:
Hi,
The current code does not fix the problems with ytex. We are not able to
install it.
In particular, the line 248 in pom.xml yields the following error
Artifact has not been packaged yet. When used on reactor artifact, copy should
be executed after packaging: see MDEP-187.
(org.apache.maven.plugins:maven-dependency-plugin:2.8:copy-dependencies:copy-dependencies:package)
And mvn install produces another error
C:\cTakes-3.2.2\ctakes\ctakes-ytex>mvn install [INFO] Scanning for projects...
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES YTEX 3.2.3-SNAPSHOT [INFO]
------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.480 s
[INFO] Finished at: 2015-05-14T20:06:34-04:00 [INFO] Final Memory: 11M/308M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project ctakes-ytex: Could not resolve
dependencies for project org.apache.ctakes:ctakes-ytex:jar:3.2.3-SNAPSHOT:
Failed to collect dependencies at
org.apache.ctakes:ctakes-ytex-res:jar:3.2.3-SNAPSHOT: Failed to read artifact
descriptor for org.apache.ctakes:ctakes-ytex-res:jar:3.2.3-SNAPSHOT: Failure to
find org.apache.ctakes:ctakes:pom:3.2.3-SNAPSHOT in
https://urldefense.proofpoint.com/v2/url?u=http-3A__repository.apache.org_snapshots&d=BQIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=oYnNHlu9WeyIAouO2sbC8rwnO7qyKWL8DH09M599zrY&s=Bkp2DPH1dHC0DhhI9VYawWCMM_l-qG16-MIjLCQIu34&e=
was cached in the local repository, resolution will not be reattempted until
the update interval of apache.snapshots has elapsed or updates are forced ->
[Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run
Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please
read the following articles:
[ERROR] [Help 1]
https://urldefense.proofpoint.com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_MAVEN_DependencyResolutionException&d=BQIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=oYnNHlu9WeyIAouO2sbC8rwnO7qyKWL8DH09M599zrY&s=su8nCLnSwmBw5afAxgqYyNE9f3jjwKtfWULyH2qViNg&e=
I do not understand why it is trying to build 3.2.3-SNAPSHOT.
Michal
-----Message d'origine-----
De : Pei Chen [mailto:[email protected]] Envoyé : May-13-15 10:38 AM À :
[email protected]<mailto:[email protected]>
Objet : [VOTE] Release Apache cTAKES 3.2.2 (rc2)
This is a call for a vote on releasing the following candidate (rc2) as Apache
cTAKES 3.2.2.
The major change since rc1 was to include the fix for CTAKES-359 - UMLS
Authentication failing despite correct username and password.
For more detailed information on the changes/release notes, please visit:
https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_secure_ReleaseNote.jspa-3FprojectId-3D12313621-26version-3D12328717&d=BQIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=oYnNHlu9WeyIAouO2sbC8rwnO7qyKWL8DH09M599zrY&s=yW0xKvuvrECwTPLK5ULU8E2_vDSXWnI6Ce8opcrrfHQ&e=
The release was made using the cTAKES release process documented here:
https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_repos_asf_ctakes_site_backup_content_ctakes-2Drelease-2Dguide.mdtext&d=BQIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=oYnNHlu9WeyIAouO2sbC8rwnO7qyKWL8DH09M599zrY&s=BNeUAGZdT6hX50H5OA9NJlOm-vTMsDnHzcyYWcxzbYs&e=
The candidate is available at:
https://urldefense.proofpoint.com/v2/url?u=https-3A__dist.apache.org_repos_dist_dev_ctakes_ctakes-2D3.2.2-2Drc2_apache-2Dctakes-2D3.2.2-2Dsrc.tar.gz&d=BQIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=oYnNHlu9WeyIAouO2sbC8rwnO7qyKWL8DH09M599zrY&s=XQWcrUPH-rN7g7eyx7-rApZjBFYweSbPCJ8q9TLQby8&e=
/.zip
The tag to be voted on:
https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_repos_asf_ctakes_tags_ctakes-2D3.2.2-2Drc2&d=BQIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=oYnNHlu9WeyIAouO2sbC8rwnO7qyKWL8DH09M599zrY&s=okabPEFslTTq_6NiJohmIqPEj2L_3-oEbpsS-bsaxxM&e=
The MD5 checksum of the tarball can be found at:
https://urldefense.proofpoint.com/v2/url?u=https-3A__dist.apache.org_repos_dist_dev_ctakes_ctakes-2D3.2.2-2Drc2_apache-2Dctakes-2D3.2.2-2Dsrc.tar.gz.md5&d=BQIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=oYnNHlu9WeyIAouO2sbC8rwnO7qyKWL8DH09M599zrY&s=q_4YoxfjfMJuMOsiKti1-Tz2BtX3blijWTnUAJOwdio&e=
/.zip.md5
The signature of the tarball can be found at:
https://urldefense.proofpoint.com/v2/url?u=https-3A__dist.apache.org_repos_dist_dev_ctakes_ctakes-2D3.2.2-2Drc2_apache-2Dctakes-2D3.2.2-2Dsrc.tar.gz.asc&d=BQIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=oYnNHlu9WeyIAouO2sbC8rwnO7qyKWL8DH09M599zrY&s=4h3BpNFfg6q0tHNQepfsSoa4kXEF8Zn1-1XggzEAYK0&e=
/.zip.asc
Apache cTAKES' KEYS file, containing the PGP keys used to sign the release:
https://urldefense.proofpoint.com/v2/url?u=https-3A__dist.apache.org_repos_dist_release_ctakes_KEYS&d=BQIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=oYnNHlu9WeyIAouO2sbC8rwnO7qyKWL8DH09M599zrY&s=ILgWbVhZSwXrNYT36TiIZBok0DgwDL6s9Qqir5uaUEk&e=
Please vote on releasing these packages as Apache cTAKES 3.2.2. The vote is
open for at least the next 72 hours.
The vote passes if at least three binding +1 votes are cast.
[ ] +1 Release the packages as Apache cTAKES 3.2.2 [ ] -1 Do not release the
packages because...
Also, the convenience binary can be found at:
https://urldefense.proofpoint.com/v2/url?u=https-3A__dist.apache.org_repos_dist_dev_ctakes_ctakes-2D3.2.2-2Drc2_apache-2Dctakes-2D3.2.2-2Dbin.tar.gz.md5&d=BQIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=oYnNHlu9WeyIAouO2sbC8rwnO7qyKWL8DH09M599zrY&s=n_JrZ0ewFs9cvhWcsA9RZemrdWQ5JfiEAHULvQ53LVo&e=
/.zip
[INFO] Error stacktraces are turned on.
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for
org.apache.ctakes:ctakes-assertion:jar:3.2.3-SNAPSHOT
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must
be unique: junit:junit:jar -> duplicate declaration of version (?) @
org.apache.ctakes:ctakes-assertion:[unknown-version],
C:\Apps\cTakes-3.2.2\ctakes\ctakes-assertion\pom.xml, line 146, column 15
[WARNING] 'dependencies.dependency.systemPath' for
org.mitre.medfacts:medfacts-i2b2:jar should not point at files within the
project directory, ${project.basedir}/lib/med-facts-i2b2-1.2-SNAPSHOT.jar will
be unresolvable by dependent projects @
org.apache.ctakes:ctakes-assertion:[unknown-version],
C:\Apps\cTakes-3.2.2\ctakes\ctakes-assertion\pom.xml, line 185, column 16
[WARNING] 'dependencies.dependency.systemPath' for
org.mitre.medfacts:medfacts-zoner:jar should not point at files within the
project directory, ${project.basedir}/lib/med-facts-zoner-1.1.jar will be
unresolvable by dependent projects @
org.apache.ctakes:ctakes-assertion:[unknown-version],
C:\Apps\cTakes-3.2.2\ctakes\ctakes-assertion\pom.xml, line 192, column 16
[WARNING] 'dependencies.dependency.systemPath' for
org.mitre.jcarafe.core:jcarafe.core:jar should not point at files within the
project directory, ${project.basedir}/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar
will be unresolvable by dependent projects @
org.apache.ctakes:ctakes-assertion:[unknown-version],
C:\Apps\cTakes-3.2.2\ctakes\ctakes-assertion\pom.xml, line 199, column 16
[WARNING] 'dependencies.dependency.systemPath' for
org.mitre.jcarafe.ext:jcarafe.ext:jar should not point at files within the
project directory, ${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar
will be unresolvable by dependent projects @
org.apache.ctakes:ctakes-assertion:[unknown-version],
C:\Apps\cTakes-3.2.2\ctakes\ctakes-assertion\pom.xml, line 206, column 16
[WARNING]
[WARNING] Some problems were encountered while building the effective model for
org.apache.ctakes:ctakes-distribution:pom:3.2.3-SNAPSHOT
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must
be unique: org.apache.ctakes:ctakes-ne-contexts:jar -> duplicate declaration of
version (?) @ org.apache.ctakes:ctakes-distribution:[unknown-version],
C:\Apps\cTakes-3.2.2\ctakes\ctakes-distribution\pom.xml, line 103, column 15
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten
the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support
building such malformed projects.
[WARNING]
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES YTEX 3.2.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- jaxb2-maven-plugin:1.6:xjc (default) @ ctakes-ytex ---
[INFO] No changes detected in schema or binding files - skipping source
generation.
[INFO]
[INFO] --- maven-remote-resources-plugin:1.4:process (default) @ ctakes-ytex ---
[INFO]
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @
ctakes-ytex ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copying 3 resources
[INFO]
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-ytex ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @
ctakes-ytex ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 16 resources
[INFO] Copying 3 resources
[INFO]
[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @
ctakes-ytex ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (default-test) @ ctakes-ytex ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ ctakes-ytex ---
[INFO] Building jar:
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\ctakes-ytex-3.2.3-SNAPSHOT.jar
[INFO]
[INFO] --- maven-site-plugin:3.1:attach-descriptor (attach-descriptor) @
ctakes-ytex ---
[INFO]
[INFO] --- maven-dependency-plugin:2.8:copy-dependencies (copy-dependencies) @
ctakes-ytex ---
[INFO] Copying jaxb-api-2.2.5.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\jaxb-api-2.2.5.jar
[INFO] Copying junit-4.10.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\junit-4.10.jar
[INFO] Copying spring-aop-3.1.2.RELEASE.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\spring-aop-3.1.2.RELEASE.jar
[INFO] Copying java-cup-0.11a.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\java-cup-0.11a.jar
[INFO] Copying hamcrest-core-1.1.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\hamcrest-core-1.1.jar
[INFO] Copying dom4j-1.6.1.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\dom4j-1.6.1.jar
[INFO] Copying aspectjweaver-1.7.3.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\aspectjweaver-1.7.3.jar
[INFO] Copying spring-core-3.1.2.RELEASE.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\spring-core-3.1.2.RELEASE.jar
[INFO] Copying ehcache-core-2.4.6.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\ehcache-core-2.4.6.jar
[INFO] Copying jboss-logging-3.1.0.GA.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\jboss-logging-3.1.0.GA.jar
[INFO] Copying ctakes-ytex-res-3.2.3-SNAPSHOT.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\ctakes-ytex-res-3.2.3-SNAPSHOT.jar
[INFO] Copying spring-orm-3.1.2.RELEASE.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\spring-orm-3.1.2.RELEASE.jar
[INFO] Copying spring-tx-3.1.2.RELEASE.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\spring-tx-3.1.2.RELEASE.jar
[INFO] Copying commons-jxpath-1.3.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\commons-jxpath-1.3.jar
[INFO] Copying spring-expression-3.1.2.RELEASE.jar to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\lib\spring-expression-3.1.2.RELEASE.jar
[INFO] spring-beans-3.1.2.RELEASE.jar already exists in destination.
[INFO] jboss-transaction-api_1.1_spec-1.0.1.Final.jar already exists in
destination.
[INFO] jsr305-1.3.9.jar already exists in destination.
[INFO] commons-beanutils-1.8.3.jar already exists in destination.
[INFO] hibernate-commons-annotations-4.0.2.Final.jar already exists in
destination.
[INFO] log4j-1.2.16.jar already exists in destination.
[INFO] ant-launcher-1.9.2.jar already exists in destination.
[INFO] commons-logging-1.1.1.jar already exists in destination.
[INFO] commons-lang-2.4.jar already exists in destination.
[INFO] guava-10.0.jar already exists in destination.
[INFO] hibernate-core-4.2.6.Final.jar already exists in destination.
[INFO] commons-dbcp-1.4.jar already exists in destination.
[INFO] solr-commons-csv-3.5.0.jar already exists in destination.
[INFO] mysql-connector-java-5.1.26.jar already exists in destination.
[INFO] weka-stable-3.6.10.jar already exists in destination.
[INFO] spring-asm-3.1.2.RELEASE.jar already exists in destination.
[INFO] jchronic-0.2.6.jar already exists in destination.
[INFO] xml-apis-1.0.b2.jar already exists in destination.
[INFO] slf4j-api-1.6.1.jar already exists in destination.
[INFO] slf4j-log4j12-1.6.1.jar already exists in destination.
[INFO] commons-pool-1.5.4.jar already exists in destination.
[INFO] antlr-2.7.7.jar already exists in destination.
[INFO] hibernate-jpa-2.0-api-1.0.1.Final.jar already exists in destination.
[INFO] spring-jdbc-3.1.2.RELEASE.jar already exists in destination.
[INFO] jaxb-impl-2.2.5.jar already exists in destination.
[INFO] aopalliance-1.0.jar already exists in destination.
[INFO] spring-context-3.1.2.RELEASE.jar already exists in destination.
[INFO] commons-cli-1.2.jar already exists in destination.
[INFO] javassist-3.15.0-GA.jar already exists in destination.
[INFO] ant-1.9.2.jar already exists in destination.
[INFO] ant-contrib-1.0b3.jar already exists in destination.
[INFO] hibernate-ehcache-4.2.6.Final.jar already exists in destination.
[INFO] hsqldb-1.8.0.10.jar already exists in destination.
[INFO]
[INFO] --- maven-antrun-plugin:1.6:run (generate-config) @ ctakes-ytex ---
[INFO] Executing tasks
main:
templateToConfig.init:
templateToConfig.extractTemplates:
templateToConfig.updateConfig:
[echo] config.source.dir =
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex/../ctakes-ytex-res/src/main/resources
[echo] config.generated.dir =
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\classes
[copy] Copying 6 files to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\classes
templateToConfig:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-antrun-plugin:1.6:run (generate-test-config) @ ctakes-ytex ---
[INFO] Executing tasks
main:
generateTestYtexProperties:
[echo]
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\test-classes/org/apache/ctakes/ytex/ytex.properties
exists, skipping test ytex.properties generation
templateToConfig.init:
templateToConfig.extractTemplates:
templateToConfig.updateConfig:
[echo] config.source.dir =
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex/../ctakes-ytex-res/src/main/resources
[echo] config.generated.dir =
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\test-classes
[copy] Copying 6 files to
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\test-classes
templateToConfig:
deleteTestDb:
[delete] Deleting directory
C:\Users\iglemi01\AppData\Local\Temp\ctakes-test-hsqldb\ctakes
test.setup:
init:
umls.check.mrconso:
[echo] umls.schema PUBLIC
[echo] umls.catalog
[sql] Executing commands
[sql] 1 of 1 SQL statements executed successfully
[echo] mrconso.out = 0
[echo]
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\mrconso-check.txt
[echo] mrconso.exists = ${mrconso.exists}
umls.all:
[echo] mrconso.exists = ${mrconso.exists}
init:
umls.drop.view:
[echo] drop v_snomed_fword_lookup table
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema PUBLIC
[echo] umls.catalog
[echo] execute ./hsql/./umls/drop_view.sql
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[echo] executing C:\Users\iglemi01\AppData\Local\Temp\ytex733673900.sql
[sql] Executing resource:
C:\Users\iglemi01\AppData\Local\Temp\ytex733673900.sql
[sql] 3 of 3 SQL statements executed successfully
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex733673900.sql
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex1145058032use.sql
init.conn:
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
umls.create.view:
[echo] create the v_snomed_fword_lookup table
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema PUBLIC
[echo] umls.catalog
[echo] execute ./hsql/./umls/create_view.sql
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[echo] executing C:\Users\iglemi01\AppData\Local\Temp\ytex851701425.sql
[sql] Executing resource:
C:\Users\iglemi01\AppData\Local\Temp\ytex851701425.sql
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex851701425.sql
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex747878751use.sql
umls.import.view:
[echo] import v_snomed_fword_lookup from
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\scripts\data/umls/v_snomed_fword_lookup.txt.
Be patient, this can take a while.
jdl:
[echo] jdl.format
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\scripts\data/umls/v_snomed_fword_lookup.xml
[echo] jdl.data
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\scripts\data/umls/v_snomed_fword_lookup.txt
[echo] umls.prefix
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[java] 2015-05-15 20:57:51,800 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2015-05-15 20:57:51,820 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - insert into
PUBLIC.v_snomed_fword_lookup (cui,tui,fword,fstem,tok_str,stem_str) values
(?,?,?,?,?,?)
[java] 2015-05-15 20:57:52,580 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2733 rows total
umls.index.view:
[echo] index the v_snomed_fword_lookup table
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema PUBLIC
[echo] umls.catalog
[echo] execute ./hsql/./umls/index_view.sql
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[echo] executing C:\Users\iglemi01\AppData\Local\Temp\ytex1999732540.sql
[sql] Executing resource:
C:\Users\iglemi01\AppData\Local\Temp\ytex1999732540.sql
[sql] 4 of 4 SQL statements executed successfully
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex1999732540.sql
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex1816778988use.sql
umls.setup.dump:
uima.drop:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema PUBLIC
[echo] umls.catalog
[echo] execute ./hsql/uima/drop_view.sql
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[echo] executing C:\Users\iglemi01\AppData\Local\Temp\ytex552573288.sql
[sql] Executing resource:
C:\Users\iglemi01\AppData\Local\Temp\ytex552573288.sql
[sql] 9 of 9 SQL statements executed successfully
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex552573288.sql
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex119937349use.sql
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema PUBLIC
[echo] umls.catalog
[echo] execute ./hsql/uima/drop_document.sql
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[echo] executing C:\Users\iglemi01\AppData\Local\Temp\ytex582153258.sql
[sql] Executing resource:
C:\Users\iglemi01\AppData\Local\Temp\ytex582153258.sql
[sql] 29 of 29 SQL statements executed successfully
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex582153258.sql
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex1701437720use.sql
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema PUBLIC
[echo] umls.catalog
[echo] execute ./hsql/uima/drop_reference.sql
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[echo] executing C:\Users\iglemi01\AppData\Local\Temp\ytex1480085.sql
[sql] Executing resource:
C:\Users\iglemi01\AppData\Local\Temp\ytex1480085.sql
[sql] 7 of 7 SQL statements executed successfully
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex1480085.sql
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex244893008use.sql
uima.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema PUBLIC
[echo] umls.catalog
[echo] execute ./hsql/uima/create_reference.sql
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[echo] executing C:\Users\iglemi01\AppData\Local\Temp\ytex569626832.sql
[sql] Executing resource:
C:\Users\iglemi01\AppData\Local\Temp\ytex569626832.sql
[sql] 10 of 10 SQL statements executed successfully
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex569626832.sql
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex504443840use.sql
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema PUBLIC
[echo] umls.catalog
[echo] execute ./hsql/uima/create_document.sql
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[echo] executing C:\Users\iglemi01\AppData\Local\Temp\ytex814096196.sql
[sql] Executing resource:
C:\Users\iglemi01\AppData\Local\Temp\ytex814096196.sql
[sql] 36 of 36 SQL statements executed successfully
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex814096196.sql
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex1094484317use.sql
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema PUBLIC
[echo] umls.catalog
[echo] execute ./hsql/uima/create_view.sql
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[echo] executing C:\Users\iglemi01\AppData\Local\Temp\ytex558958167.sql
[sql] Executing resource:
C:\Users\iglemi01\AppData\Local\Temp\ytex558958167.sql
[sql] 5 of 5 SQL statements executed successfully
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex558958167.sql
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex1095810660use.sql
uima.create.trigger:
init:
init.conn:
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
uima.ref.load:
jdl:
[echo] jdl.format ref_uima_type.xml
[echo] jdl.data ref_uima_type.txt
[echo] umls.prefix
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[java] 2015-05-15 20:58:16,366 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2015-05-15 20:58:16,386 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_uima_type
(uima_type_id,uima_type_name,table_name) values (?,?,?)
[java] 2015-05-15 20:58:16,936 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 38 rows total
init:
init.conn:
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
uima.examples.load:
jdl:
[echo] jdl.format examples/fracture_demo.xml
[echo] jdl.data examples/fracture_demo.txt
[echo] umls.prefix
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[java] 2015-05-15 20:58:38,416 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2015-05-15 20:58:38,436 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.fracture_demo
(site_id,note_text,fracture,note_set) values (?,?,?,?)
[java] 2015-05-15 20:58:39,016 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,016 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,016 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,016 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,016 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,016 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,016 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,016 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,026 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,026 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,026 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,026 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,026 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,026 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,026 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 2 rows
[java] 2015-05-15 20:58:39,026 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 31 rows total
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema PUBLIC
[echo] umls.catalog
[echo] execute ./hsql/uima/fracture_demo.sql
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[echo] executing C:\Users\iglemi01\AppData\Local\Temp\ytex794681274.sql
[sql] Executing resource:
C:\Users\iglemi01\AppData\Local\Temp\ytex794681274.sql
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex794681274.sql
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex406173098use.sql
init:
init.conn:
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
uima.stopword.load:
jdl:
[echo] jdl.format stopword.xml
[echo] jdl.data stopword.txt
[echo] umls.prefix
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[java] 2015-05-15 20:59:01,143 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 44 encapsulator 65534
[java] 2015-05-15 20:59:01,153 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.ref_stopword
(stopword) values (?)
[java] 2015-05-15 20:59:01,753 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - inserted 360 rows total
uima.all:
kernel.drop:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema PUBLIC
[echo] umls.catalog
[echo] execute ./hsql/kernel/drop_tables.sql
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[echo] executing C:\Users\iglemi01\AppData\Local\Temp\ytex1465938920.sql
[sql] Executing resource:
C:\Users\iglemi01\AppData\Local\Temp\ytex1465938920.sql
[sql] 22 of 22 SQL statements executed successfully
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex1465938920.sql
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex1588407068use.sql
kernel.create:
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema PUBLIC
[echo] umls.catalog
[echo] execute ./hsql/kernel/create_tables.sql
[copy] Copying 1 file to C:\Users\iglemi01\AppData\Local\Temp
[echo] executing C:\Users\iglemi01\AppData\Local\Temp\ytex1385106610.sql
[sql] Executing resource:
C:\Users\iglemi01\AppData\Local\Temp\ytex1385106610.sql
[sql] 52 of 52 SQL statements executed successfully
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex1385106610.sql
[delete] Deleting: C:\Users\iglemi01\AppData\Local\Temp\ytex858755123use.sql
kernel.all:
all:
[INFO] Executed tasks
[INFO]
[INFO] --- maven-surefire-plugin:2.12.1:test (surefire-it) @ ctakes-ytex ---
[INFO] Surefire report directory:
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\surefire-reports
-------------------------------------------------------
T E S T S
-------------------------------------------------------
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.apache.ctakes.jdl.AppJdlTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.42 sec
Running org.apache.ctakes.jdl.AppMainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.39 sec
Running org.apache.ctakes.jdl.AppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec
Running org.apache.ctakes.jdl.common.FileUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.29 sec
Running org.apache.ctakes.jdl.common.PropertiesFileTest
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec
Running org.apache.ctakes.jdl.common.PropFileTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec
Running org.apache.ctakes.jdl.common.SingletonTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 sec
Running org.apache.ctakes.jdl.data.base.JdlConnectionTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.38 sec
Running org.apache.ctakes.jdl.data.loader.CsvLoaderTest
2015-05-15 20:59:09,033 INFO org.apache.ctakes.jdl.data.loader.CsvLoader -
delimiter 44 encapsulator 65534
2015-05-15 20:59:09,063 INFO org.apache.ctakes.jdl.data.loader.CsvLoader -
delimiter 59 encapsulator 65534
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.53 sec
Running org.apache.ctakes.jdl.data.loader.XmlLoaderTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.49 sec
Running org.apache.ctakes.jdl.data.xml.DomParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 sec
Running org.apache.ctakes.jdl.data.xml.DomUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.23 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBindTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.52 sec
Running org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtilTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.52 sec
Running org.apache.ctakes.jdl.data.xml.ValidationTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.38 sec
Running org.apache.ctakes.ytex.ConceptDaoTest
2015-05-15 20:59:15,413 INFO
org.springframework.context.support.ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@6d994bd3:
startup date [Fri May 15 20:59:15 EDT 2015]; root of context hierarchy
2015-05-15 20:59:15,473 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from URL
[jar:file:/C:/Users/iglemi01/.m2/repository/org/apache/ctakes/ctakes-ytex-res/3.2.3-SNAPSHOT/ctakes-ytex-res-3.2.3-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]
2015-05-15 20:59:15,543 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from URL
[file:/C:/Apps/cTakes-3.2.2/ctakes/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]
2015-05-15 20:59:15,553 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Overriding bean definition for bean 'kernelApplicationContext': replacing
[Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[jar:file:/C:/Users/iglemi01/.m2/repository/org/apache/ctakes/ctakes-ytex-res/3.2.3-SNAPSHOT/ctakes-ytex-res-3.2.3-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]
with [Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[file:/C:/Apps/cTakes-3.2.2/ctakes/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]
2015-05-15 20:59:15,573 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Pre-instantiating singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@313eadd5:
defining beans [kernelApplicationContext]; root of factory hierarchy
2015-05-15 20:59:15,643 INFO
org.springframework.context.support.ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@5e9384fb:
startup date [Fri May 15 20:59:15 EDT 2015]; root of context hierarchy
2015-05-15 20:59:15,643 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-datasource.xml]
2015-05-15 20:59:15,703 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2015-05-15 20:59:15,733 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.xml]
2015-05-15 20:59:15,913 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex-default.properties]
2015-05-15 20:59:15,913 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
2015-05-15 20:59:15,923 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex-umls.properties]
2015-05-15 20:59:15,953 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Pre-instantiating singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@64186d33:
defining beans
[org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService];
root of factory hierarchy
2015-05-15 20:59:15,993 INFO
org.springframework.beans.factory.config.PropertiesFactoryBean - Loading
properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
2015-05-15 20:59:16,653 INFO org.hibernate.annotations.common.Version -
HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2015-05-15 20:59:16,653 INFO org.hibernate.Version - HHH000412: Hibernate
Core {4.2.6.Final}
2015-05-15 20:59:16,663 INFO org.hibernate.cfg.Environment - HHH000206:
hibernate.properties not found
2015-05-15 20:59:16,663 INFO org.hibernate.cfg.Environment - HHH000021:
Bytecode provider name : javassist
2015-05-15 20:59:17,355 INFO org.hibernate.dialect.Dialect - HHH000400: Using
dialect: org.hibernate.dialect.HSQLDialect
2015-05-15 20:59:17,365 INFO
org.hibernate.engine.jdbc.internal.LobCreatorBuilder - HHH000423: Disabling
contextual LOB creation as JDBC driver reported JDBC version [3] less than 4
2015-05-15 20:59:17,475 INFO
org.hibernate.engine.transaction.internal.TransactionFactoryInitiator -
HHH000399: Using default transaction strategy (direct JDBC transactions)
2015-05-15 20:59:17,475 INFO
org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using
ASTQueryTranslatorFactory
2015-05-15 20:59:17,815 INFO org.hibernate.cache.spi.UpdateTimestampsCache -
HHH000250: Starting update timestamps cache at region:
org.hibernate.cache.spi.UpdateTimestampsCache
2015-05-15 20:59:17,825 INFO org.hibernate.cache.internal.StandardQueryCache
- HHH000248: Starting query cache at region:
org.hibernate.cache.internal.StandardQueryCache
2015-05-15 20:59:18,435 INFO
org.springframework.orm.hibernate4.HibernateTransactionManager - Using
DataSource [org.apache.commons.dbcp.BasicDataSource@2648873] of Hibernate
SessionFactory for HibernateTransactionManager
2015-05-15 20:59:18,795 INFO
org.springframework.cache.ehcache.EhCacheManagerFactoryBean - Initializing
EHCache CacheManager
2015-05-15 20:59:18,815 WARN net.sf.ehcache.CacheManager - Creating a new
instance of CacheManager using the diskStorePath
"C:\Users\iglemi01\AppData\Local\Temp\" which is already used by an existing
CacheManager.
The source of the configuration was
net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigurationSource@1cfe4382.
The diskStore path for this CacheManager will be set to
C:\Users\iglemi01\AppData\Local\Temp\\ehcache_auto_created_1431737958805.
To avoid this warning consider using the CacheManager factory methods to create
a singleton CacheManager or specifying a separate ehcache configuration
(ehcache.xml) for each CacheManager instance.
Create concept graph
2015-05-15 20:59:19,095 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
- could not load conceptGraph from classpath, attempt to load from:
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\test-classes\org\apache\ctakes\ytex\conceptGraph\test.gz
2015-05-15 20:59:19,095 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
-
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\test-classes\org\apache\ctakes\ytex\conceptGraph\test.gz
not found, cannot load concept graph
2015-05-15 20:59:19,095 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
- could not load conceptGraph: test
2015-05-15 20:59:19,095 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
- createConceptGraph(): file not found, creating concept graph from database.
2015-05-15 20:59:19,095 DEBUG org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
- roots: [root]
2015-05-15 20:59:19,095 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
- computing intrinsic info for concept graph: test
2015-05-15 20:59:19,095 INFO
org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl - computing
subsumer counts
2015-05-15 20:59:19,095 INFO
org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl - computing
max leaves
2015-05-15 20:59:19,095 INFO
org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl - computing
leaf counts
2015-05-15 20:59:19,095 INFO
org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl - storing
intrinsic ic
2015-05-15 20:59:19,095 DEBUG
org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl - cat=2.0
2015-05-15 20:59:19,095 DEBUG
org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl - root=0.0
2015-05-15 20:59:19,095 DEBUG
org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl -
bacteria=1.415037499278844
2015-05-15 20:59:19,095 DEBUG
org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl -
vertebrate=1.263034405833794
2015-05-15 20:59:19,095 DEBUG
org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl - dog=2.0
2015-05-15 20:59:19,095 DEBUG
org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl - e coli=2.0
2015-05-15 20:59:19,095 DEBUG
org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl - animal=1.0
2015-05-15 20:59:19,095 INFO
org.apache.ctakes.ytex.kernel.IntrinsicInfoContentEvaluatorImpl - finished
computing intrinsic ic
2015-05-15 20:59:19,095 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
- writing concept graph:
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\test-classes\org\apache\ctakes\ytex\conceptGraph\test.gz
2015-05-15 20:59:19,155 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
- loading concept graph from
file:/C:/Apps/cTakes-3.2.2/ctakes/ctakes-ytex/target/test-classes/org/apache/ctakes/ytex/conceptGraph/test.gz
2015-05-15 20:59:19,175 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
- concept graph test, vertices: 7
2015-05-15 20:59:19,175 INFO
org.springframework.context.support.ClassPathXmlApplicationContext - Closing
ApplicationContext 'kernelApplicationContext': startup date [Fri May 15
20:59:15 EDT 2015]; root of context hierarchy
2015-05-15 20:59:19,185 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Destroying singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@64186d33:
defining beans
[org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService];
root of factory hierarchy
2015-05-15 20:59:19,185 INFO
org.springframework.cache.ehcache.EhCacheManagerFactoryBean - Shutting down
EHCache CacheManager
2015-05-15 20:59:19,365 INFO
org.springframework.context.support.ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@241377b6:
startup date [Fri May 15 20:59:19 EDT 2015]; root of context hierarchy
2015-05-15 20:59:19,365 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from URL
[jar:file:/C:/Users/iglemi01/.m2/repository/org/apache/ctakes/ctakes-ytex-res/3.2.3-SNAPSHOT/ctakes-ytex-res-3.2.3-SNAPSHOT.jar!/org/apache/ctakes/ytex/simSvcBeanRefContext.xml]
2015-05-15 20:59:19,365 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from URL
[file:/C:/Apps/cTakes-3.2.2/ctakes/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/simSvcBeanRefContext.xml]
2015-05-15 20:59:19,375 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Overriding bean definition for bean 'kernelApplicationContext': replacing
[Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[jar:file:/C:/Users/iglemi01/.m2/repository/org/apache/ctakes/ctakes-ytex-res/3.2.3-SNAPSHOT/ctakes-ytex-res-3.2.3-SNAPSHOT.jar!/org/apache/ctakes/ytex/simSvcBeanRefContext.xml]]
with [Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[file:/C:/Apps/cTakes-3.2.2/ctakes/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/simSvcBeanRefContext.xml]]
2015-05-15 20:59:19,375 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Pre-instantiating singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@28872a84:
defining beans [kernelApplicationContext]; root of factory hierarchy
2015-05-15 20:59:19,385 INFO
org.springframework.context.support.ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@7ce37f76:
startup date [Fri May 15 20:59:19 EDT 2015]; root of context hierarchy
2015-05-15 20:59:19,385 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-datasource.xml]
2015-05-15 20:59:19,415 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2015-05-15 20:59:19,435 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.xml]
2015-05-15 20:59:19,495 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel-sim.xml]
2015-05-15 20:59:19,535 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex-default.properties]
2015-05-15 20:59:19,535 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
2015-05-15 20:59:19,535 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex-umls.properties]
2015-05-15 20:59:19,555 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Pre-instantiating singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@58e1c345:
defining beans
[org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService,conceptSimilarityService,abstractConceptKernel,abstractLinKernel,abstractSemanticSimKernel,mainSuiSemanticTypeKernel,tuiSemanticTypeKernel,wordSenseDisambiguator];
root of factory hierarchy
2015-05-15 20:59:19,565 INFO
org.springframework.beans.factory.config.PropertiesFactoryBean - Loading
properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
2015-05-15 20:59:20,025 INFO org.hibernate.dialect.Dialect - HHH000400: Using
dialect: org.hibernate.dialect.HSQLDialect
2015-05-15 20:59:20,025 INFO
org.hibernate.engine.jdbc.internal.LobCreatorBuilder - HHH000423: Disabling
contextual LOB creation as JDBC driver reported JDBC version [3] less than 4
2015-05-15 20:59:20,035 INFO
org.hibernate.engine.transaction.internal.TransactionFactoryInitiator -
HHH000399: Using default transaction strategy (direct JDBC transactions)
2015-05-15 20:59:20,035 INFO
org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using
ASTQueryTranslatorFactory
2015-05-15 20:59:20,045 INFO org.hibernate.cache.spi.UpdateTimestampsCache -
HHH000250: Starting update timestamps cache at region:
org.hibernate.cache.spi.UpdateTimestampsCache
2015-05-15 20:59:20,045 INFO org.hibernate.cache.internal.StandardQueryCache
- HHH000248: Starting query cache at region:
org.hibernate.cache.internal.StandardQueryCache
2015-05-15 20:59:20,245 INFO
org.springframework.orm.hibernate4.HibernateTransactionManager - Using
DataSource [org.apache.commons.dbcp.BasicDataSource@1e26bf02] of Hibernate
SessionFactory for HibernateTransactionManager
2015-05-15 20:59:20,335 INFO
org.springframework.cache.ehcache.EhCacheManagerFactoryBean - Initializing
EHCache CacheManager
2015-05-15 20:59:20,345 WARN net.sf.ehcache.CacheManager - Creating a new
instance of CacheManager using the diskStorePath
"C:\Users\iglemi01\AppData\Local\Temp\" which is already used by an existing
CacheManager.
The source of the configuration was
net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigurationSource@35c1b25e.
The diskStore path for this CacheManager will be set to
C:\Users\iglemi01\AppData\Local\Temp\\ehcache_auto_created_1431737960345.
To avoid this warning consider using the CacheManager factory methods to create
a singleton CacheManager or specifying a separate ehcache configuration
(ehcache.xml) for each CacheManager instance.
2015-05-15 20:59:20,515 INFO
org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - begin
initialization for concept graph: test
2015-05-15 20:59:20,525 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
- loading concept graph from
file:/C:/Apps/cTakes-3.2.2/ctakes/ctakes-ytex/target/test-classes/org/apache/ctakes/ytex/conceptGraph/test.gz
2015-05-15 20:59:20,525 INFO org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl
- concept graph test, vertices: 7
2015-05-15 20:59:20,525 INFO
org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl -
initializing similarity measures
2015-05-15 20:59:20,525 INFO
org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl - end
initialization for concept graph: test
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.412 sec
Running org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
2015-05-15 20:59:21,785 INFO
org.springframework.context.support.ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@6f3a342a:
startup date [Fri May 15 20:59:21 EDT 2015]; root of context hierarchy
2015-05-15 20:59:21,845 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from URL
[jar:file:/C:/Users/iglemi01/.m2/repository/org/apache/ctakes/ctakes-ytex-res/3.2.3-SNAPSHOT/ctakes-ytex-res-3.2.3-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]
2015-05-15 20:59:21,915 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from URL
[file:/C:/Apps/cTakes-3.2.2/ctakes/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]
2015-05-15 20:59:21,915 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Overriding bean definition for bean 'kernelApplicationContext': replacing
[Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[jar:file:/C:/Users/iglemi01/.m2/repository/org/apache/ctakes/ctakes-ytex-res/3.2.3-SNAPSHOT/ctakes-ytex-res-3.2.3-SNAPSHOT.jar!/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]
with [Generic bean: class
[org.springframework.context.support.ClassPathXmlApplicationContext]; scope=;
abstract=false; lazyInit=false; autowireMode=0; dependencyCheck=0;
autowireCandidate=true; primary=false; factoryBeanName=null;
factoryMethodName=null; initMethodName=null; destroyMethodName=null; defined in
URL
[file:/C:/Apps/cTakes-3.2.2/ctakes/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernelBeanRefContext.xml]]
2015-05-15 20:59:21,945 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Pre-instantiating singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@1f800b16:
defining beans [kernelApplicationContext]; root of factory hierarchy
2015-05-15 20:59:22,005 INFO
org.springframework.context.support.ClassPathXmlApplicationContext -
Refreshing
org.springframework.context.support.ClassPathXmlApplicationContext@3aead8a8:
startup date [Fri May 15 20:59:22 EDT 2015]; root of context hierarchy
2015-05-15 20:59:22,005 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-datasource.xml]
2015-05-15 20:59:22,075 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.hbm.xml]
2015-05-15 20:59:22,105 INFO
org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML
bean definitions from class path resource
[org/apache/ctakes/ytex/beans-kernel.xml]
2015-05-15 20:59:22,285 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex-default.properties]
2015-05-15 20:59:22,285 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
2015-05-15 20:59:22,285 INFO
org.springframework.beans.factory.config.PropertyPlaceholderConfigurer -
Loading properties file from class path resource
[org/apache/ctakes/ytex/ytex-umls.properties]
2015-05-15 20:59:22,335 INFO
org.springframework.beans.factory.support.DefaultListableBeanFactory -
Pre-instantiating singletons in
org.springframework.beans.factory.support.DefaultListableBeanFactory@6ada5bd7:
defining beans
[org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0,ytexProperties,hibernateProperties,dataSource,txAdvice,txTemplate,txTemplateNew,transactionManager,sessionFactory,org.springframework.aop.config.internalAutoProxyCreator,daoOperation,umlsDaoOperation,exporterOperation,wekaImporter,mapperOperation,treeOperation,utilOperation,corpusEvaluatorOperation,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#0,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#1,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#2,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#3,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#4,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#5,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#6,org.springframework.aop.support.DefaultBeanFactoryPointcutAdvisor#7,kernelEvaluationDao,conceptDao,umlsDao,wekaBagOfWordsExporter,gramMatrixExporter,documentResultInstanceImporter,wekaResultsImporter,classifierEvaluationDao,libSVMGramMatrixExporter,rGramMatrixExporter,libsvmUtil,instanceTreeBuilder,abstractNormKernel,equalityKernel,atttributeProductKernel,cacheManager,abstractCorpusKernelEvaluator,foldGenerator,kernelUtil,baseClassifierEvaluationParser,semiLEvaluationParser,libSVMParser,svmLightParser,svmlinParser,ClassifierEvaluationImporter,sparseDataExporter,sparseDataFormatterFactory,svmLightFormatterFactory,libSVMFormatterFactory,svmLinFormatterFactory,sgtFormatterFactory,sparseMatrixFormatterFactory,semiLFormatterFactory,wekaFormatterFactory,instanceDataExporter,infogainAttributeEval,rankerSearch,infogainAttributeSelection,wekaAttributeEvaluator,infoContentEvaluator,intrinsicInfoContentEvaluator,imputedFeatureEvaluator,cytoscapeHelper,abstractKernelCacheAdvice,pageRankService];
root of factory hierarchy
2015-05-15 20:59:22,375 INFO
org.springframework.beans.factory.config.PropertiesFactoryBean - Loading
properties file from class path resource
[org/apache/ctakes/ytex/ytex.properties]
2015-05-15 20:59:23,025 INFO org.hibernate.annotations.common.Version -
HCANN000001: Hibernate Commons Annotations {4.0.2.Final}
2015-05-15 20:59:23,025 INFO org.hibernate.Version - HHH000412: Hibernate
Core {4.2.6.Final}
2015-05-15 20:59:23,025 INFO org.hibernate.cfg.Environment - HHH000206:
hibernate.properties not found
2015-05-15 20:59:23,025 INFO org.hibernate.cfg.Environment - HHH000021:
Bytecode provider name : javassist
2015-05-15 20:59:23,855 INFO org.hibernate.dialect.Dialect - HHH000400: Using
dialect: org.hibernate.dialect.HSQLDialect
2015-05-15 20:59:23,865 INFO
org.hibernate.engine.jdbc.internal.LobCreatorBuilder - HHH000423: Disabling
contextual LOB creation as JDBC driver reported JDBC version [3] less than 4
2015-05-15 20:59:23,975 INFO
org.hibernate.engine.transaction.internal.TransactionFactoryInitiator -
HHH000399: Using default transaction strategy (direct JDBC transactions)
2015-05-15 20:59:23,975 INFO
org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory - HHH000397: Using
ASTQueryTranslatorFactory
2015-05-15 20:59:24,205 INFO org.hibernate.cache.spi.UpdateTimestampsCache -
HHH000250: Starting update timestamps cache at region:
org.hibernate.cache.spi.UpdateTimestampsCache
2015-05-15 20:59:24,205 INFO org.hibernate.cache.internal.StandardQueryCache
- HHH000248: Starting query cache at region:
org.hibernate.cache.internal.StandardQueryCache
2015-05-15 20:59:24,835 INFO
org.springframework.orm.hibernate4.HibernateTransactionManager - Using
DataSource [org.apache.commons.dbcp.BasicDataSource@7a380c5a] of Hibernate
SessionFactory for HibernateTransactionManager
2015-05-15 20:59:25,175 INFO
org.springframework.cache.ehcache.EhCacheManagerFactoryBean - Initializing
EHCache CacheManager
2015-05-15 20:59:25,195 WARN net.sf.ehcache.CacheManager - Creating a new
instance of CacheManager using the diskStorePath
"C:\Users\iglemi01\AppData\Local\Temp\" which is already used by an existing
CacheManager.
The source of the configuration was
net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigurationSource@199574a6.
The diskStore path for this CacheManager will be set to
C:\Users\iglemi01\AppData\Local\Temp\\ehcache_auto_created_1431737965195.
To avoid this warning consider using the CacheManager factory methods to create
a singleton CacheManager or specifying a separate ehcache configuration
(ehcache.xml) for each CacheManager instance.
2015-05-15 20:59:25,515 WARN org.hibernate.engine.jdbc.spi.SqlExceptionHelper
- SQL Error: -22, SQLState: S0002
2015-05-15 20:59:25,515 ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper
- Table not found in statement [select top ? mrconso0_.aui as col_0_0_,
mrconso0_.str as col_1_0_ from PUBLIC.MRCONSO mrconso0_ where mrconso0_.aui>?
and length(mrconso0_.aui)>0 and length(mrconso0_.str)<200 and
mrconso0_.lat='ENG' order by mrconso0_.aui]
2015-05-15 20:59:25,525 WARN org.apache.ctakes.ytex.umls.dao.UMLSDaoTest -
sql exception - mrconso probably doesn't exist, check error
org.hibernate.exception.SQLGrammarException: could not prepare statement
at
org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:123)
at
org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49)
at
org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:125)
at
org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:188)
at
org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryStatement(StatementPreparerImpl.java:159)
at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1859)
at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1836)
at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1816)
at org.hibernate.loader.Loader.doQuery(Loader.java:900)
at
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:342)
at org.hibernate.loader.Loader.doList(Loader.java:2526)
at org.hibernate.loader.Loader.doList(Loader.java:2512)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2342)
at org.hibernate.loader.Loader.list(Loader.java:2337)
at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:495)
at
org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:357)
at
org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:195)
at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1269)
at org.hibernate.internal.QueryImpl.list(QueryImpl.java:101)
at
org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl.getAllAuiStr(UMLSDaoImpl.java:104)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at
org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:319)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at
org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:90)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy11.getAllAuiStr(Unknown Source)
at
org.apache.ctakes.ytex.umls.dao.UMLSDaoTest.testGetAllAuiStr(UMLSDaoTest.java:53)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at
org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:45)
at
org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
at
org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:42)
at
org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
at
org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:263)
at
org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:68)
at
org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:47)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:231)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:60)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:229)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:50)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:222)
at org.junit.runners.ParentRunner.run(ParentRunner.java:300)
at
org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:249)
at
org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:142)
at
org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:113)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at
org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
at
org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165)
at
org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85)
at
org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:104)
at
org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75)
Caused by: java.sql.SQLException: Table not found in statement [select top ?
mrconso0_.aui as col_0_0_, mrconso0_.str as col_1_0_ from PUBLIC.MRCONSO
mrconso0_ where mrconso0_.aui>? and length(mrconso0_.aui)>0 and
length(mrconso0_.str)<200 and mrconso0_.lat='ENG' order by mrconso0_.aui]
at org.hsqldb.jdbc.Util.throwError(Unknown Source)
at org.hsqldb.jdbc.jdbcPreparedStatement.<init>(Unknown Source)
at org.hsqldb.jdbc.jdbcConnection.prepareStatement(Unknown Source)
at
org.apache.commons.dbcp.DelegatingConnection.prepareStatement(DelegatingConnection.java:281)
at
org.apache.commons.dbcp.PoolingDataSource$PoolGuardConnectionWrapper.prepareStatement(PoolingDataSource.java:313)
at
org.hibernate.engine.jdbc.internal.StatementPreparerImpl$5.doPrepare(StatementPreparerImpl.java:161)
at
org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:182)
... 60 more
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4 sec
Results :
Tests run: 36, Failures: 0, Errors: 0, Skipped: 4
[INFO]
[INFO] --- maven-install-plugin:2.3.1:install (default-install) @ ctakes-ytex
---
[INFO] Installing
C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\target\ctakes-ytex-3.2.3-SNAPSHOT.jar
to
C:\Users\iglemi01\.m2\repository\org\apache\ctakes\ctakes-ytex\3.2.3-SNAPSHOT\ctakes-ytex-3.2.3-SNAPSHOT.jar
[INFO] Installing C:\Apps\cTakes-3.2.2\ctakes\ctakes-ytex\pom.xml to
C:\Users\iglemi01\.m2\repository\org\apache\ctakes\ctakes-ytex\3.2.3-SNAPSHOT\ctakes-ytex-3.2.3-SNAPSHOT.pom
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:19 min
[INFO] Finished at: 2015-05-15T20:59:26-04:00
[INFO] Final Memory: 35M/335M
[INFO] ------------------------------------------------------------------------
